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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ), 'gf_id' => 'HOM05D001197', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001197' ), 'data_identifier' => 'HOM05D001197', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001197', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '92' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p14590' => 'bna', 'A03p26670' => 'bna', 'A05p27780' => 'bna', 'A10p11860' => 'bna', 'Aa31LG11G10690' => 'aar', 'Aa31LG3G10520' => 'aar', 'Aa31LG4G15140' => 'aar', 'Aa31LG4G3740' => 'aar', 'Aa31LG5G22940' => 'aar', 'Aa31LG5G8730' => 'aar', 'Aa31LG6G2450' => 'aar', 'Aa31LG8G7750' => 'aar', 'Actinidia03783' => 'ach', 'Actinidia13129' => 'ach', 'Actinidia18590' => 'ach', 'Actinidia18876' => 'ach', 'Actinidia23472' => 'ach', 'Actinidia25365' => 'ach', 'Actinidia34691' => 'ach', 'Ah.04g165160' => 'amhyb', 'Ah.07g202960' => 'amhyb', 'Ah.08g211050' => 'amhyb', 'AL215U10020' => 'aly', 'AL2G33280' => 'aly', 'AL3G34890' => 'aly', 'AL6G30390' => 'aly', 'AL7G33830' => 'aly', 'AL8G30030' => 'aly', 'Aqoxy2G01237' => 'aox', 'Aqoxy2G02026' => 'aox', 'Aqoxy2G02035' => 'aox', 'Aqoxy3G04122' => 'aox', 'Aqoxy4G01909' => 'aox', 'Aqoxy5G00393' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0XQ1R2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8IP2CM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EHT4FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K1P89V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K4K5W1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MXVB7A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PV01EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QW9ZFX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RESD80' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U017VK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYB2LV' => 'arhy', 'AT1G73530' => 'ath', 'AT2G27330' => 'ath', 'AT2G37510' => 'ath', 'AT3G20930' => 'ath', 'AT4G20030' => 'ath', 'AT5G19030' => 'ath', 'AT5G54580' => 'ath', 'AT5G59860' => 'ath', 'ATR0222G027' => 'atr', 'ATR0559G200' => 'atr', 'ATR0564G395' => 'atr', 'ATR0626G402' => 'atr', 'ATR0807G033' => 'atr', 'Atru.chr10.2245' => 'acertr', 'Atru.chr12.997' => 'acertr', 'Atru.chr2.3111' => 'acertr', 'Atru.chr2.3134' => 'acertr', 'Atru.chr4.2577' => 'acertr', 'Atru.chr8.1954' => 'acertr', 'Atru.chr9.1575' => 'acertr', 'AUR62002954' => 'cqu', 'AUR62006242' => 'cqu', 'AUR62007759' => 'cqu', 'AUR62029268' => 'cqu', 'AUR62032806' => 'cqu', 'AUR62041146' => 'cqu', 'BcaB01g03066' => 'bca', 'BcaB01g04299' => 'bca', 'BcaB01g04879' => 'bca', 'BcaB01g05288' => 'bca', 'BcaB02g10085' => 'bca', 'BcaB03g15716' => 'bca', 'BcaB06g26170' => 'bca', 'BcaB08g35815' => 'bca', 'BcaC01g04934' => 'bca', 'BcaC01g06312' => 'bca', 'BcaC04g20327' => 'bca', 'BcaC05g28206' => 'bca', 'BcaC06g30641' => 'bca', 'BcaC08g45639' => 'bca', 'BcaC09g51349' => 'bca', 'BcaNung03488' => 'bca', 'BolC1t01370H' => 'bol', 'BolC2t07304H' => 'bol', 'BolC2t09159H' => 'bol', 'BolC3t13553H' => 'bol', 'BolC3t14115H' => 'bol', 'BolC3t15537H' => 'bol', 'BolC4t23923H' => 'bol', 'BolC5t33042H' => 'bol', 'BolC6t38513H' => 'bol', 'BolC7t45572H' => 'bol', 'BolC9t57362H' => 'bol', 'BraA01t01125Z' => 'bra', 'BraA03t10246Z' => 'bra', 'BraA03t10749Z' => 'bra', 'BraA03t11878Z' => 'bra', 'BraA05t19814Z' => 'bra', 'BraA05t21665Z' => 'bra', 'BraA10t43283Z' => 'bra', 'C01p14030' => 'bna', 'C02p31160' => 'bna', 'C03p17030' => 'bna', 'C03p31950' => 'bna', 'C05p43120' => 'bna', 'C07p50690' => 'bna', 'C09p44900' => 'bna', 'CAN.G1299.3' => 'can', 'CANSAT01G1479' => 'cansat', 'CANSAT01G2455' => 'cansat', 'CANSAT35G1291' => 'cansat', 'CARHR066530' => 'chi', 'CARHR096810' => 'chi', 'CARHR119920' => 'chi', 'CARHR226820' => 'chi', 'CARHR267860' => 'chi', 'Carub.0002s1020' => 'cru', 'Carub.0002s1021' => 'cru', 'Carub.0002s1022' => 'cru', 'Carub.0002s2027' => 'cru', 'Carub.0003s2091' => 'cru', 'Carub.0004s0796' => 'cru', 'Carub.0005s1188' => 'cru', 'Carub.0006s1735' => 'cru', 'Carub.0006s2750' => 'cru', 'Carub.0007s2110' => 'cru', 'Carub.0008s1484' => 'cru', 'Carub.0008s2060' => 'cru', 'Ca_08784_v3' => 'car', 'Ca_10508_v3' => 'car', 'Ca_18835_v3' => 'car', 'Ca_21589_v3' => 'car', 'Ca_30094_v3' => 'car', 'Cc00_g18860' => 'ccan', 'Cc01_g12400' => 'ccan', 'Cc01_g12420' => 'ccan', 'Cc04_g08840' => 'ccan', 'Cc05_g13030' => 'ccan', 'CDE02G0017' => 'cde', 'CDE05G1032' => 'cde', 'CDE11G0878' => 'cde', 'Cfa011257' => 'cfa', 'Cfa011456' => 'cfa', 'Cfa020683' => 'cfa', 'Ciclev10006073m.g' => 'ccl', 'Ciclev10016768m.g' => 'ccl', 'Ciclev10022555m.g' => 'ccl', 'Ciclev10023396m.g' => 'ccl', 'Ciclev10024110m.g' => 'ccl', 'Ciclev10029617m.g' => 'ccl', 'Ciclev10029673m.g' => 'ccl', 'Ciclev10031772m.g' => 'ccl', 'CiPaw.02G092000' => 'cil', 'CiPaw.12G015900' => 'cil', 'CiPaw.12G125100' => 'cil', 'CiPaw.13G098300' => 'cil', 'CiPaw.14G032500' => 'cil', 'CiPaw.15G151100' => 'cil', 'ClCG03G001920' => 'cla', 'ClCG04G008400' => 'cla', 'ClCG04G012480' => 'cla', 'ClCG08G008180' => 'cla', 'COL.COLO4_00311' => 'col', 'COL.COLO4_00312' => 'col', 'COL.COLO4_14854' => 'col', 'COL.COLO4_18460' => 'col', 'COL.COLO4_28874' => 'col', 'Cpa.g.c32761' => 'cpa', 'Cpa.g.sc156.9' => 'cpa', 'Cpa.g.sc16.28' => 'cpa', 'Cpa.g.sc190.24' => 'cpa', 'Cpa.g.sc21.60' => 'cpa', 'Cpa.g.sc30.128' => 'cpa', 'CsaV3_1G005220' => 'csa', 'CsaV3_4G024750' => 'csa', 'CsaV3_5G030700' => 'csa', 'CsaV3_6G004150' => 'csa', 'CSS0002532' => 'camsi', 'CSS0004629' => 'camsi', 'CSS0006129' => 'camsi', 'CSS0009375' => 'camsi', 'CSS0018921' => 'camsi', 'CSS0033308' => 'camsi', 'CSS0041514' => 'camsi', 'CSS0048572' => 'camsi', 'DCAR_001285' => 'dca', 'DCAR_009251' => 'dca', 'DCAR_028401' => 'dca', 'DCAR_029694' => 'dca', 'Dinv02037' => 'din', 'Dinv06778' => 'din', 'Dinv08286' => 'din', 'Dinv31175' => 'din', 'Dinv32842' => 'din', 'Dinv35634' => 'din', 'Dinv37203' => 'din', 'Dinv38389' => 'din', 'Duzib093G0167' => 'dzi', 'Duzib128G1987' => 'dzi', 'Duzib151G1196' => 'dzi', 'Duzib168G2036' => 'dzi', 'ECA233G1672' => 'eca', 'ECA236G1727' => 'eca', 'ECA238G2317' => 'eca', 'ECA238G3853' => 'eca', 'EL10Ac6g13232' => 'bvu', 'EL10Ac6g14541' => 'bvu', 'Eucgr.A01243' => 'egr', 'Eucgr.B03825' => 'egr', 'Eucgr.F03395' => 'egr', 'Eucgr.G02699' => 'egr', 'Eucgr.H00611' => 'egr', 'Eucgr.J02066' => 'egr', 'FAN01G1755' => 'fan', 'FAN03G2112' => 'fan', 'FAN04G2377' => 'fan', 'FAN06G1201' => 'fan', 'FAN08G2917' => 'fan', 'FAN10G3262' => 'fan', 'FAN11G0074' => 'fan', 'FAN11G1225' => 'fan', 'FAN13G2954' => 'fan', 'FAN16G0665' => 'fan', 'FAN16G1681' => 'fan', 'FAN18G0184' => 'fan', 'FAN25G1495' => 'fan', 'FvH4_3g12730' => 'fve', 'FvH4_3g35150' => 'fve', 'FvH4_5g18110' => 'fve', 'FvH4_7g05760' => 'fve', 'Glyma.03G172300' => 'gma', 'Glyma.05G133302' => 'gma', 'Glyma.06G263200' => 'gma', 'Glyma.09G167800' => 'gma', 'Glyma.11G010600' => 'gma', 'Glyma.12G139200' => 'gma', 'Glyma.13G333700' => 'gma', 'Glyma.15G040500' => 'gma', 'Glyma.16G217600' => 'gma', 'Glyma.19G173200' => 'gma', 'Glyma.20G187000' => 'gma', 'Gohir.A01G220000' => 'ghi', 'Gohir.A01G220800' => 'ghi', 'Gohir.A02G029000' => 'ghi', 'Gohir.A04G080400' => 'ghi', 'Gohir.D01G209000' => 'ghi', 'Gohir.D02G036800' => 'ghi', 'Gorai.002G254200' => 'gra', 'Gorai.005G040700' => 'gra', 'Gorai.012G101600' => 'gra', 'GSVIVG01011252001' => 'vvi', 'GSVIVG01012134001' => 'vvi', 'GSVIVG01012135001' => 'vvi', 'GSVIVG01017884001' => 'vvi', 'GSVIVG01025020001' => 'vvi', 'GSVIVG01025527001' => 'vvi', 'GSVIVG01029394001' => 'vvi', 'HanXRQChr05g0134271' => 'han', 'HanXRQChr07g0196051' => 'han', 'HanXRQChr08g0217801' => 'han', 'HanXRQChr08g0217811' => 'han', 'HanXRQChr14g0433281' => 'han', 'HanXRQChr14g0440121' => 'han', 'Haze_02528' => 'cav', 'Haze_02531' => 'cav', 'Haze_18990' => 'cav', 'Hma1.2p1_0088F.1_g045050' => 'hma', 'Hma1.2p1_0246F.1_g101620' => 'hma', 'Hma1.2p1_0493F.1_g165030' => 'hma', 'Hma1.2p1_0624F.1_g191310' => 'hma', 'Hma1.2p1_1064F.1_g253640' => 'hma', 'Hma1.2p1_1065F.1_g253730' => 'hma', 'HPP92_000798' => 'vpl', 'HPP92_002398' => 'vpl', 'HPP92_005942' => 'vpl', 'HPP92_005958' => 'vpl', 'HPP92_011832' => 'vpl', 'HPP92_016546' => 'vpl', 'HPP92_026544' => 'vpl', 'Hund05872' => 'sun', 'Hund20454' => 'sun', 'Hund20728' => 'sun', 'Hund23356' => 'sun', 'Hund27848' => 'sun', 'Hund27852' => 'sun', 'Lalb_Chr01g0006241' => 'lal', 'Lalb_Chr02g0151701' => 'lal', 'Lalb_Chr03g0030211' => 'lal', 'Lalb_Chr14g0375031' => 'lal', 'Lalb_Chr20g0113221' => 'lal', 'Lalb_Chr22g0353761' => 'lal', 'Lj1C1148T2' => 'lonja', 'Lj1g0023993' => 'lja', 'Lj2C31G3' => 'lonja', 'Lj2g0011934' => 'lja', 'Lj3g0009978' => 'lja', 'Lj4g0014495' => 'lja', 'Lj4g0020607' => 'lja', 'Lj5g0027704' => 'lja', 'Lsat_1_v5_gn_2_111720' => 'lsa', 'Lsat_1_v5_gn_2_11821' => 'lsa', 'Lsat_1_v5_gn_2_60840' => 'lsa', 'Lsat_1_v5_gn_8_23841' => 'lsa', 'Lsat_1_v5_gn_8_77780' => 'lsa', 'Lsat_1_v5_gn_9_94900' => 'lsa', 'Manes.02G224200' => 'mes', 'Manes.09G086900' => 'mes', 'Manes.10G057900' => 'mes', 'Manes.15G022650' => 'mes', 'Manes.15G079200' => 'mes', 'MBI08_g09791_MAGBIO' => 'mbi', 'MBI14_g24309_MAGBIO' => 'mbi', 'MBI17_g01570_MAGBIO' => 'mbi', 'MBI17_g12017_MAGBIO' => 'mbi', 'MD02G1255600' => 'mdo', 'MD04G1122000' => 'mdo', 'MD06G1236600' => 'mdo', 'MD10G1228700' => 'mdo', 'MD11G1229900' => 'mdo', 'MD12G1138600' => 'mdo', 'Medtr1g092860' => 'mtr', 'Medtr2g096560' => 'mtr', 'Medtr4g081510' => 'mtr', 'Medtr4g081520' => 'mtr', 'Medtr4g117350' => 'mtr', 'Medtr6g477870' => 'mtr', 'Medtr7g099940' => 'mtr', 'MELO3C001961.2' => 'cme', 'MELO3C003109.2' => 'cme', 'MELO3C019891.2' => 'cme', 'Migut.D02054' => 'egut', 'Migut.F00903' => 'egut', 'Migut.G00263' => 'egut', 'Migut.J00360' => 'egut', 'MSTRG.10019' => 'ama', 'MSTRG.27530' => 'ama', 'MSTRG.4327' => 'ama', 'MSTRG.5684' => 'ama', 'Nitab4.5_0000011g0090' => 'nta', 'Nitab4.5_0000202g0180' => 'nta', 'Nitab4.5_0000216g0060' => 'nta', 'Nitab4.5_0000443g0150' => 'nta', 'Nitab4.5_0001377g0010' => 'nta', 'Nitab4.5_0001437g0210' => 'nta', 'Nitab4.5_0002594g0010' => 'nta', 'Nitab4.5_0003782g0140' => 'nta', 'Nitab4.5_0008708g0030' => 'nta', 'Nitab4.5_0012407g0010' => 'nta', 'Nitab4.5_0025924g0010' => 'nta', 'Nn2g12601' => 'nnu', 'Nn2g12919' => 'nnu', 'Nn6g34956' => 'nnu', 'Nn7g38294' => 'nnu', 'Oeu020535.2' => 'oeu', 'Oeu030505.1' => 'oeu', 'Oeu049901.1' => 'oeu', 'Oeu060050.3' => 'oeu', 'Os02g0730800' => 'osa', 'Os03g0278800' => 'osa', 'Os04g0583800' => 'osa', 'Peaxi162Scf00173g00825' => 'pax', 'Peaxi162Scf00199g00924' => 'pax', 'Peaxi162Scf00358g00512' => 'pax', 'Peaxi162Scf00604g00422' => 'pax', 'Peaxi162Scf00769g00028' => 'pax', 'PGR004G0745' => 'pgr', 'PGR004G0965' => 'pgr', 'PGR004G1304' => 'pgr', 'PGR031G2783' => 'pgr', 'PGR083G2829' => 'pgr', 'PGR142G0464' => 'pgr', 'PGSC0003DMG400008817' => 'stu', 'PGSC0003DMG400009433' => 'stu', 'PGSC0003DMG400011058' => 'stu', 'PGSC0003DMG400019468' => 'stu', 'PGSC0003DMG400021811' => 'stu', 'PGSC0003DMG400030795' => 'stu', 'Phvul.001G170000' => 'pvu', 'Phvul.004G143300' => 'pvu', 'Phvul.007G103400' => 'pvu', 'Phvul.011G145700' => 'pvu', 'Phvul.L003243' => 'pvu', 'Potri.001G236200' => 'ptr', 'Potri.003G074900' => 'ptr', 'Potri.008G022200' => 'ptr', 'Potri.008G022280' => 'ptr', 'Potri.010G237200' => 'ptr', 'Potri.012G038200' => 'ptr', 'Prupe.1G207800' => 'ppe', 'Prupe.2G070500' => 'ppe', 'Prupe.2G080000' => 'ppe', 'Prupe.2G080400' => 'ppe', 'Prupe.4G116100' => 'ppe', 'Prupe.5G241100' => 'ppe', 'Prupe.6G135700' => 'ppe', 'Psat1g031480' => 'psa', 'Psat3g005320' => 'psa', 'Psat3g048880' => 'psa', 'Psat4g032200' => 'psa', 'Psat6g177560' => 'psa', 'PSO063G5578' => 'pso', 'PSO339G3256' => 'pso', 'PSO384G1608' => 'pso', 'PSO478G4134' => 'pso', 'PSO648G0051' => 'pso', 'PSO675G3859' => 'pso', 'PSO675G5048' => 'pso', 'PSO782G3055' => 'pso', 'PSO832G1124' => 'pso', 'QL01p033075' => 'qlo', 'QL04p043550' => 'qlo', 'QL04p043776' => 'qlo', 'QL04p044560' => 'qlo', 'QL04p044720' => 'qlo', 'QL04p077986' => 'qlo', 'QL06p005338' => 'qlo', 'QL08p014444' => 'qlo', 'QL08p060742' => 'qlo', 'RcHm_v2.0_Chr1g0332801' => 'rch', 'RcHm_v2.0_Chr1g0338951' => 'rch', 'RcHm_v2.0_Chr1g0343161' => 'rch', 'RcHm_v2.0_Chr3g0467261' => 'rch', 'RcHm_v2.0_Chr5g0033051' => 'rch', 'RcHm_v2.0_Chr7g0177501' => 'rch', 'RcHm_v2.0_Chr7g0194881' => 'rch', 'Rhsim01G0024900' => 'rsi', 'Rhsim01G0225000' => 'rsi', 'Rhsim02G0169500' => 'rsi', 'Rhsim03G0101200' => 'rsi', 'Rhsim04G0154200' => 'rsi', 'Sabra03G0045600' => 'sbr', 'Sabra10G0185700' => 'sbr', 'Sabra12G0026500' => 'sbr', 'SalBow2G1129' => 'sbo', 'SalBow3G1707' => 'sbo', 'SalBow7G0273' => 'sbo', 'SalBow8G2066' => 'sbo', 'Sc06g0002260' => 'sci', 'Sc12g0001650' => 'sci', 'Sc17g0004160' => 'sci', 'Sc19g0004590' => 'sci', 'Sc20g0004630' => 'sci', 'Sed0010178' => 'sed', 'Sed0013914' => 'sed', 'Sed0025992' => 'sed', 'SEGI_02071' => 'sgi', 'SEGI_04061' => 'sgi', 'SEGI_12369' => 'sgi', 'SGA_v2.0_scaffold164G38122' => 'sas', 'SGA_v2.0_scaffold39G15373' => 'sas', 'SGA_v2.0_scaffold51G18673' => 'sas', 'SGA_v2.0_scaffold7G03940' => 'sas', 'SHI12626' => 'shi', 'Solyc02g068440.3' => 'sly', 'Solyc06g035610.3' => 'sly', 'Solyc06g054380.4' => 'sly', 'Solyc09g011210.4' => 'sly', 'Solyc10g084630.2' => 'sly', 'Solyc11g007160.2' => 'sly', 'Solyc11g073238.1' => 'sly', 'Sopen02g017580' => 'spe', 'Sopen06g019450' => 'spe', 'Sopen09g005950' => 'spe', 'Sopen10g034070' => 'spe', 'Sopen11g003080' => 'spe', 'Sp3g18960' => 'spa', 'Sp5g15580' => 'spa', 'Sp5g28690' => 'spa', 'Sp6g16530' => 'spa', 'Sp6g25350' => 'spa', 'Sp7g18490' => 'spa', 'TAR164G0001' => 'tar', 'TAR369G0886' => 'tar', 'TAR623G0161' => 'tar', 'TAR623G1766' => 'tar', 'TAR624G1015' => 'tar', 'TAR624G1208' => 'tar', 'TAR628G0436' => 'tar', 'TAR628G1289' => 'tar', 'TAR629G2713' => 'tar', 'TAR629G3306' => 'tar', 'THA.LOC104798716' => 'tha', 'THA.LOC104802742' => 'tha', 'THA.LOC104810247' => 'tha', 'Thecc.05G044200' => 'tca', 'Thecc.10G108300' => 'tca', 'Thhalv10002114m.g' => 'esa', 'Thhalv10014796m.g' => 'esa', 'Thhalv10014908m.g' => 'esa', 'Thhalv10015391m.g' => 'esa', 'Thhalv10019191m.g' => 'esa', 'Thhalv10020913m.g' => 'esa', 'Thhalv10026477m.g' => 'esa', 'TPR.G18707' => 'tpr', 'TPR.G20133' => 'tpr', 'TPR.G21460' => 'tpr', 'TPR.G24059' => 'tpr', 'TPR.G34295' => 'tpr', 'TPR.G36221' => 'tpr', 'TWI15G0442' => 'twi', 'TWI38G2166' => 'twi', 'TWI53G1683' => 'twi', 'TWI73G1277' => 'twi', 'TWI79G0169' => 'twi', 'TWI79G1193' => 'twi', 'unitig_744.g24187' => 'ugi', 'unitig_899.g14476' => 'ugi', 'vmacro08668' => 'vma', 'vmacro11010' => 'vma', 'vmacro14509' => 'vma', 'VMungo0464G1095' => 'vmu', 'VMungo0720G1910' => 'vmu', 'VMungo1127G2071' => 'vmu', 'VMungo1383G0574' => 'vmu', 'Zm00001eb012660' => 'zma', 'Zm00001eb253560' => 'zma', 'Zm00001eb416760' => 'zma', 'Zm00001eb428060' => 'zma' ) $gf_id = 'HOM05D001197' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001197' ) $data_identifier = 'HOM05D001197' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 8, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 6, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 5, 'acertr' => (int) 7, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 11, 'bra' => (int) 7, 'can' => (int) 1, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 12, 'car' => (int) 5, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 8, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 6, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 7, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 2, 'lja' => (int) 6, 'lsa' => (int) 6, 'mes' => (int) 5, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 6, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 9, 'qlo' => (int) 9, 'rch' => (int) 7, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 4, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 3, 'sas' => (int) 4, 'shi' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 10, 'tha' => (int) 3, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 6, 'twi' => (int) 6, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb428060' $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